Contacts of the helix formed by residues 200 - 205 (chain D) in PDB entry 2ONK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 200 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C HIS* 3.5 16.7 - - + -
100C THR* 3.7 13.0 - - - +
200C PHE* 4.0 20.0 - + - -
201C GLY* 3.7 19.5 - - - -
204C VAL* 5.0 0.9 - - + -
218C TYR* 6.0 2.2 - + - -
199D GLU* 1.3 80.0 - - - +
201D GLY* 1.3 73.5 + - - +
202D ALA 3.5 0.7 - - - -
203D VAL* 2.9 7.7 + - - +
204D VAL* 2.9 52.8 + - + +
208D TYR* 6.4 0.9 - + - -
214D PRO* 3.9 8.5 - - + -
215D THR* 3.6 37.0 - - + -
218D TYR* 3.2 44.4 - + + -
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Residues in contact with GLY 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C HIS* 4.7 1.8 - - - -
200C PHE* 3.7 26.1 - - - -
99D HIS* 4.0 13.4 - - - +
100D THR* 4.4 2.2 - - - -
199D GLU* 3.6 2.5 + - - -
200D PHE* 1.3 82.2 - - - +
202D ALA* 1.3 64.9 + - - +
203D VAL 3.0 1.0 + - - -
204D VAL* 3.1 8.7 - - - +
205D VAL* 3.0 24.3 - - - +
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Residues in contact with ALA 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D HIS* 3.4 23.2 + - - +
102D ALA* 4.1 6.1 - - + -
103D GLY* 3.4 18.0 - - - +
106D LEU* 5.0 0.9 - - + -
134D ALA* 4.1 9.6 - - + +
138D VAL* 3.9 19.3 - - + -
199D GLU* 2.6 28.7 + - + +
201D GLY* 1.3 72.1 - - - +
203D VAL* 1.3 61.9 + - - +
205D VAL 3.9 1.7 + - - -
206D ILE* 3.4 18.9 - - - +
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Residues in contact with VAL 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D GLY 5.6 0.2 - - - +
131D ILE* 4.2 28.3 - - + +
134D ALA* 3.5 21.8 - - + -
135D MET* 4.2 15.9 - - + -
199D GLU* 3.6 29.6 - - + +
200D PHE* 2.9 8.2 + - - +
202D ALA* 1.3 74.5 - - - +
204D VAL* 1.3 56.8 + - + +
206D ILE* 2.5 32.6 + - - +
207D ALA 3.0 23.0 + - - +
210D PRO 5.6 0.2 - - - +
212D ILE* 5.0 12.3 - - + +
215D THR* 5.6 3.1 - - - +
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Residues in contact with VAL 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C PHE* 4.9 5.2 - - + -
218C TYR* 4.3 23.1 - - + +
200D PHE* 2.9 56.2 + - + +
201D GLY* 3.1 20.2 - - - +
203D VAL* 1.3 72.9 - - + +
205D VAL* 1.3 76.7 + - + +
206D ILE 3.0 5.2 + - - -
207D ALA 3.3 8.2 + - - -
208D TYR* 3.2 33.5 + - + +
215D THR* 3.6 16.4 - - + +
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Residues in contact with VAL 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C TYR* 4.6 14.1 - - + -
221C TYR* 3.5 37.3 + - + -
100D THR* 4.4 16.8 - - + +
103D GLY* 3.3 35.2 - - - +
104D ILE* 3.4 12.1 - - + +
107D LEU* 3.5 13.7 - - + +
201D GLY* 3.0 22.2 - - - +
202D ALA 4.1 0.4 - - - +
203D VAL 2.8 2.2 + - - -
204D VAL* 1.3 79.7 - - + +
206D ILE* 1.3 60.1 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il